Ordered changes in histone modifications at the core of the Arabidopsis circadian clock

Proceedings of the National Academy of Sciences of the United States of America

Volumn 109, Issue 52, 2012, Pages 21540-21545

  Malapeira, Jordi ^a   Khaitova, Lucie Crhak ^a   Mas, Paloma ^a  

^a UNIVERSITY OF BARCELONA   (Spain)

Author keywords

Circadian rhythms; Histone acetylation; Histone methylation

Indexed keywords

HISTONE H3; HISTONE METHYLTRANSFERASE;

ARABIDOPSIS; ARTICLE; CHROMATIN ASSEMBLY AND DISASSEMBLY; CIRCADIAN RHYTHM; GENE ACTIVATION; GENE EXPRESSION; GENE EXPRESSION REGULATION; GENE REPRESSION; HISTONE ACETYLATION; HISTONE METHYLATION; HISTONE MODIFICATION; NONHUMAN; OSCILLATION; PRIORITY JOURNAL;

ARABIDOPSIS; ARABIDOPSIS PROTEINS; CIRCADIAN CLOCKS; GENE EXPRESSION REGULATION, PLANT; GENES, PLANT; HISTONE-LYSINE N-METHYLTRANSFERASE; HISTONES; LYSINE; METHYLATION; PROTEIN BINDING; PROTEIN PROCESSING, POST-TRANSLATIONAL; REPRESSOR PROTEINS;

ARABIDOPSIS; ARABIDOPSIS THALIANA; MAMMALIA;

EID: 84871838945     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.1217022110     Document Type: Article

References (53)

1. Bannister AJ, Kouzarides T (2011) Regulation of rogram, the chromatin by histone modifications. Cell Res 21(3):381-395.
2. Klose RJ, Bird AP (2006) Genomic DNA methylation: The mark and its mediators. Trends Biochem Sci 31(2):89-97. (Pubitemid 43221841)
3. Jenuwein T, Allis CD (2001) Translating the histone code. Science 293(5532):1074-1080. (Pubitemid 32758077)
4. Ng SS, Yue WW, Oppermann U, Klose RJ (2009) Dynamic protein methylation in chromatin biology. Cell Mol Life Sci 66(3):407-422.
5. Suganuma T, Workman JL (2011) Signals and combinatorial functions of histone modifications. Annu Rev Biochem 80(1):473-499.
6. Pfluger J, Wagner D (2007) Histone modifications and dynamic regulation of genome accessibility in plants. Curr Opin Plant Biol 10(6):645-652. (Pubitemid 350030606)
7. Berr A, Shafiq S, Shen WH (2011) Histone modifications in transcriptional activation during plant development. Biochim Biophys Acta 1809(10):567-576.
8. He Y, Michaels SD, Amasino RM (2003) Regulation of flowering time by histone acetylation in Arabidopsis. Science 302(5651):1751-1754. (Pubitemid 37505736)
9. Kim J-M, et al. (2008) Alterations of lysine modifications on the histone H3 N-tail under drought stress conditions in Arabidopsis thaliana. Plant Cell Physiol 49(10):1580-1588.
10. To TK, et al. (2011) Arabidopsis HDA6 regulates locus-directed heterochromatin silencing in cooperation with MET1. PLoS Genet 7(4):e1002055.
11. Charron J-BF, He H, Elling AA, Deng XW (2009) Dynamic landscapes of four histone modifications during deetiolation in Arabidopsis. Plant Cell 21(12):3732-3748.
12. Caro E, Castellano MM, Gutierrez C (2007) A chromatin link that couples cell division to root epidermis patterning in Arabidopsis. Nature 447(7141):213-217. (Pubitemid 46763078)
13. Roudier F, et al. (2011) Integrative epigenomic mapping defines four main chromatin states in Arabidopsis. EMBO J 30(10):1928-1938.
14. Zhang X, Bernatavichute YV, Cokus S, Pellegrini M, Jacobsen SE (2009) Genome-wide analysis of mono-, di- and trimethylation of histone H3 lysine 4 in Arabidopsis thaliana. Genome Biol 10(6):R62.
15. Thorstensen T, Grini PE, Aalen RB (2011) SET domain proteins in plant development. Biochim Biophys Acta 1809(8):407-420.
16. Berr A, et al. (2010) Arabidopsis SET DOMAIN GROUP2 is required for H3K4 trimethylation and is crucial for both sporophyte and gametophyte development. Plant Cell 22(10):3232-3248.
17. Guo L, Yu Y, Law JA, Zhang X (2010) SET DOMAIN GROUP2 is the major histone H3 lysine 4 trimethyltransferase in Arabidopsis. Proc Natl Acad Sci USA 107(43):18557-18562.
18. McClung CR (2011) The genetics of plant clocks. Adv Genet 74:105-139.
19. Doherty CJ, Kay SA (2010) Circadian control of global gene expression patterns. Annu Rev Genet 44:419-444.
20. Wang ZY, Tobin EM (1998) Constitutive expression of the CIRCADIAN CLOCK ASSOCIATED 1 (CCA1) gene disrupts circadian rhythms and suppresses its own expression. Cell 93(7):1207-1217.
21. Schaffer R, et al. (1998) The late elongated hypocotyl mutation of Arabidopsis disrupts circadian rhythms and the photoperiodic control of flowering. Cell 93(7):1219-1229. (Pubitemid 28307426)
22. Matsushika A, Makino S, Kojima M, Mizuno T (2000) Circadian waves of expression of the APRR1/TOC1 family of pseudo-response regulators in Arabidopsis thaliana: Insight into the plant circadian clock. Plant Cell Physiol 41(9):1002-1012.
23. Makino S, Matsushika A, Kojima M, Yamashino T, Mizuno T (2002) The APRR1/TOC1 quintet implicated in circadian rhythms of Arabidopsis thaliana: I. Characterization with APRR1-overexpressing plants. Plant Cell Physiol 43(1):58-69. (Pubitemid 34152457)
24. Strayer CA, et al. (2000) Cloning of the Arabidopsis clock gene TOC1, an autoregulatory response regulator homolog. Science 289(5480):768-771.
25. Fowler S, et al. (1999) GIGANTEA: A circadian clock-controlled gene that regulates photoperiodic flowering in Arabidopsis and encodes a protein with several possible membrane-spanning domains. EMBO J 18(17):4679-4688. (Pubitemid 29415522)
26. Park DH, et al. (1999) Control of circadian rhythms and photoperiodic flowering by the Arabidopsis GIGANTEA gene. Science 285(5433):1579-1582. (Pubitemid 29420584)
27. Nusinow DA, et al. (2011) The ELF4-ELF3-LUX complex links the circadian clock to diurnal control of hypocotyl growth. Nature 475(7356):398-402.
28. Gendron JM, et al. (2012) Arabidopsis circadian clock protein, TOC1, is a DNA-binding transcription factor. Proc Natl Acad Sci USA 109(8):3167-3172.
29. Huang W, et al. (2012) Mapping the core of the Arabidopsis circadian clock defines the network structure of the oscillator. Science 336(6077):75-79.
30. Pokhilko A, et al. (2012) The clock gene circuit in Arabidopsis includes a repressilator with additional feedback loops. Mol Syst Biol 8:574.
31. Perales M, Más P (2007) A functional link between rhythmic changes in chromatin structure and the Arabidopsis biological clock. Plant Cell 19(7):2111-2123. (Pubitemid 47347456)
32. Farinas B, Mas P (2011) Functional implication of the MYB transcription factor RVE8/LCL5 in the circadian control of histone acetylation. Plant J 66(2):318-329.
33. Song H-R, Noh Y-S (2012) Rhythmic oscillation of histone acetylation and methylation at the Arabidopsis central clock loci. Mol Cells 34(3):279-287.
34. Jones MA, et al. (2010) Jumonji domain protein JMJD5 functions in both the plant and human circadian systems. Proc Natl Acad Sci USA 107(50):21623-21628.
35. Lu SX, et al. (2011) The Jumonji C domain-containing protein JMJ30 regulates period length in the Arabidopsis circadian clock. Plant Physiol 155(2):906-915.
36. Turck F, et al. (2007) Arabidopsis TFL2/LHP1 specifically associates with genes marked by trimethylation of histone H3 lysine 27. PLoS Genet 3(6):e86.
37. Xydous M, Sekeri-Pataryas KE, Prombona A, Sourlingas TG (2012) Nicotinamide treatment reduces the levels of histone H3K4 trimethylation in the promoter of the mper1 circadian clock gene and blocks the ability of dexamethasone to induce the acute response. Biochim Biophys Acta 1819(8):877-884.
38. Lawson M, et al. (2010) Inhibitors to understand molecular mechanisms of NAD+-dependent deacetylases (sirtuins). Biochim Biophys Acta 1799(10-12):726-739.
39. Dodd AN, et al. (2007) The Arabidopsis circadian clock incorporates a cADPR-based feedback loop. Science 318(5857):1789-1792. (Pubitemid 350274392)
40. Johnson CH, et al. (1995) Circadian oscillations of cytosolic and chloroplastic free calcium in plants. Science 269(5232):1863-1865.
41. Rankin PW, Jacobson EL, Benjamin RC, Moss J, Jacobson MK (1989) Quantitative studies of inhibitors of ADP-ribosylation in vitro and in vivo. J Biol Chem 264(8):4312-4317. (Pubitemid 19081328)
42. Biel M, Kretsovali A, Karatzali E, Papamatheakis J, Giannis A (2004) Design, synthesis, and biological evaluation of a small-molecule inhibitor of the histone acetyltransferase Gcn5. Angew Chem Int Ed Engl 43(30):3974-3976. (Pubitemid 39257485)
43. Bowers EM, et al. (2010) Virtual ligand screening of the p300/CBP histone acetyltransferase: Identification of a selective small molecule inhibitor. Chem Biol 17(5):471-482.
44. Nakamichi N, et al. (2010) PSEUDO-RESPONSE REGULATORS 9, 7, and 5 are transcriptional repressors in the Arabidopsis circadian clock. Plant Cell 22(3):594-605.
45. Lloyd AM, Schena M, Walbot V, Davis RW (1994) Epidermal cell fate determination in Arabidopsis: Patterns defined by a steroid-inducible regulator. Science 266(5184):436-439. (Pubitemid 24348963)
46. Ripperger JA, Schibler U (2006) Rhythmic CLOCK-BMAL1 binding to multiple E-box motifs drives circadian Dbp transcription and chromatin transitions. Nat Genet 38(3):369-374.
47. Etchegaray J-P, Lee C, Wade PA, Reppert SM (2003) Rhythmic histone acetylation underlies transcription in the mammalian circadian clock. Nature 421(6919):177-182. (Pubitemid 36090986)
48. Liu C, Lu F, Cui X, Cao X (2010) Histone methylation in higher plants. Annu Rev Plant Biol 61:395-420.
49. Doi M, Hirayama J, Sassone-Corsi P (2006) Circadian regulator CLOCK is a histone acetyltransferase. Cell 125(3):497-508.
50. Koike N, et al. (2012) Transcriptional architecture and chromatin landscape of the core circadian clock in mammals. Science 338(6105):349-354.
51. Portolés S, Más P (2010) The functional interplay between protein kinase CK2 and CCA1 transcriptional activity is essential for clock temperature compensation in Arabidopsis. PLoS Genet 6(11):e1001201.
52. Legnaioli T, Cuevas J, Mas P (2009) TOC1 functions as a molecular switch connecting the circadian clock with plant responses to drought. EMBO J 28(23):3745-3757.
53. Más P, Kim WY, Somers DE, Kay SA (2003) Targeted degradation of TOC1 by ZTL modulates circadian function in Arabidopsis thaliana. Nature 426(6966):567-570. (Pubitemid 37522643)